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TASSEL 5

TASSEL project is a Java platform designed for the optimized analysis of crop genomic diversity.

User Documentation

  • Reporting Tassel 5 Issues

  • Tassel 5 User Manual

  • Getting Started with rTASSEL

  • R front-end for TASSEL (rtassel)

  • Tassel 5 GBS v2 Pipeline

  • Installing / Updating Tassel using Git (recommended)

  • Executing Tassel

  • Tassel 5.0 Pipeline (Command Line Interface)

  • Tassel 5 Pipeline Tutorial

  • Tassel Pan-genome Atlas (PanA) Pipeline

  • Tassel VCAP Documentation

Developer Documentation

  • Programming Reference URLs

  • IntelliJ Setup

  • PyCharm Setup for Kipoi

  • Eclipse Setup

  • Netbeans Setup

  • Git: Branches and Pull Requests

  • Running Kotlin Scripts on CBSU

  • Guide for programming

  • Tassel 5 Architecture

  • Tassel 5 JavaDoc

  • Releasing Tassel 5 and PHG

  • Creating Tassel 5 Build from Source Code

  • Tassel 5 Logging

  • Executing Tassel 5 Unit Tests

  • Tassel 5 Self-Describing Plugins

  • Testing Tassel with JUnit

Archived User Documentation

  • Tassel 3.0 and 4.0 Pipeline (Command Line Interface)

  • Tassel 3 Pipeline Tutorial

  • Tassel GBS Pipeline

  • Tassel UNEAK Pipeline

  • Tassel and R Integration

Example Java Code

  • Reading/writing hapmap, manipulating genotype tables, writing to text file

Wiki features

Updated 2022-11-02